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In order to combine these conflicting mappings, we used the average of all the responses for each mapping and use this as the centroid of the mapping consequent.
To evaluate the accuracy of text2genome species and gene mappings, we used as a reference the set of articles where the original authors submitted sequences to GenBank.
To choose the most appropriate alignment for our mappings we used several criteria: symmetry, coverage, feature enrichment, and other method specific properties.
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In the case of angular mappings, we use the hyperbolic model of the unit disk (mathbb{D}).
The ~2 million read-mappings we used in this analysis had at least one intron and more than half a million reads had four introns or more.
To inform our choice of SNPs for fine-mapping, we used data from another pooling study on 574 SZ trios (explained in more detail below).
For comparison in both the replication and fine-mapping extended study we used 1021 ethnically matched healthy subjects, who were either blood donors or spouses of patients with osteoarthritis.
Note that, letting be a nonempty subset of Banach space and, are self-mappings of, we use to denote, that is, (1.16).
For fine-mapping, we also used the so-called LCN near isogenics lines [ 17].
Similar to the methods for Affymetrix, we used Ensembl mappings of Illumina probes for comparisons across platforms, so probes were excluded if they did not map to an Ensembl Gene ID (Build 59).
Raw data from the Beer [ 40] study was processed using the same pipeline as the Bhattacharjee study, except that we used ProbeSet mappings to Entrez Gene IDs appropriate to the specific platform used in that study (hu6800hsentrezgcdf version 12.0.0).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com